Oomen, P. J. A., Phung, T. -K. N., Weinberg, S. H., Bilchick, K. C., & Holmes, J. W. (2022). A rapid electromechanical model to predict reverse remodeling following cardiac resynchronization therapy. BIOMECHANICS AND MODELING IN MECHANOBIOLOGY, 21(1), 231-247. doi:10.1007/s10237-021-01532-7

Caggiano, L. R., Holmes, J. W., & Witzenburg, C. M. (2022). Individual variability in animal-specific hemodynamic compensation following myocardial infarction. JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY, 163, 156-166. doi:10.1016/j.yjmcc.2021.10.008

Montgomery, J., Richardson, W. J., Marsh, S., Rhett, J. M., Bustos, F., Degen, K., . . . Gourdie, R. G. (2021). The connexin 43 carboxyl terminal mimetic peptide αCT1 prompts differentiation of a collagen scar matrix in humans resembling unwounded skin. FASEB JOURNAL, 35(8). doi:10.1096/fj.202001881R

Rogers, J. D., Holmes, J. W., Saucerman, J. J., & Richardson, W. J. (2021). Mechano-chemo signaling interactions modulate matrix production by cardiac fibroblasts.. Matrix biology plus, 10, 100055. doi:10.1016/j.mbplus.2020.100055

Yin, B., Caggiano, L. R., Li, R. -C., McGowan, E., Holmes, J. W., & Ewald, S. E. (2021). Automated Spatially Targeted Optical Microproteomics Investigates Inflammatory Lesions In Situ. JOURNAL OF PROTEOME RESEARCH, 20(9), 4543-4552. doi:10.1021/acs.jproteome.1c00505

Gao, X., Abdi, M., Auger, D. A., Sun, C., Hanson, C. A., Robinson, A. A., . . . Bilchick, K. C. (2021). Cardiac Magnetic Resonance Assessment of Response to Cardiac Resynchronization Therapy and Programming Strategies. JACC-CARDIOVASCULAR IMAGING, 14(12), 2369-2383. doi:10.1016/j.jcmg.2021.06.015

Caggiano, L. R., & Holmes, J. W. (2021). A Comparison of Fiber Based Material Laws for Myocardial Scar. JOURNAL OF ELASTICITY, 145(1-2), 321-337. doi:10.1007/s10659-021-09845-5

Zeigler, A. C., Chandrabhatla, A. S., Christiansen, S. L., Nelson, A. R., Holmes, J. W., & Saucerman, J. J. (2021). Network model-based screen for FDA-approved drugs affecting cardiac fibrosis. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY, 10(4), 377-388. doi:10.1002/psp4.12599

Estrada, A. C., Yoshida, K., Saucerman, J. J., & Holmes, J. W. (2021). A multiscale model of cardiac concentric hypertrophy incorporating both mechanical and hormonal drivers of growth. BIOMECHANICS AND MODELING IN MECHANOBIOLOGY, 20(1), 293-307. doi:10.1007/s10237-020-01385-6

Yoshida, K., & Holmes, J. W. (2021). Computational models of cardiac hypertrophy. PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, 159, 75-85. doi:10.1016/j.pbiomolbio.2020.07.001

Zeigler, A. C., Nelson, A. R., Chandrabhatla, A. S., Brazhkina, O., Holmes, J. W., & Saucerman, J. J. (2020). Computational model predicts paracrine and intracellular drivers of fibroblast phenotype after myocardial infarction. MATRIX BIOLOGY, 91-92, 136-151. doi:10.1016/j.matbio.2020.03.007

Yoshida, K., McCulloch, A. D., Omens, J. H., & Holmes, J. W. (2020). Predictions of hypertrophy and its regression in response to pressure overload. BIOMECHANICS AND MODELING IN MECHANOBIOLOGY, 19(3), 1079-1089. doi:10.1007/s10237-019-01271-w

Zeigler, A., Nelson, A., Chandrabhatla, A., Brazhkina, O., Holmes, J., & Saucerman, J. (2019). Computational Model Predicts Paracrine and Intracellular Drivers of Fibroblast Phenotype After Myocardial Infarction. doi:10.1101/840017

Estrada, A. C., Yoshida, K., Clarke, S. A., & Holmes, J. W. (2020). Longitudinal Reinforcement of Acute Myocardial Infarcts Improves Function by Transmurally Redistributing Stretch and Stress. JOURNAL OF BIOMECHANICAL ENGINEERING-TRANSACTIONS OF THE ASME, 142(2). doi:10.1115/1.4044030

Phung, T. -K. N., Waters, C. D., & Holmes, J. W. (2020). Open-Source Routines for Building Personalized Left Ventricular Models From Cardiac Magnetic Resonance Imaging Data. JOURNAL OF BIOMECHANICAL ENGINEERING-TRANSACTIONS OF THE ASME, 142(2). doi:10.1115/1.4043876

Lee, J. -J., Talman, L., Peirce, S. M., & Holmes, J. W. (2019). Spatial scaling in multiscale models: methods for coupling agent-based and finite-element models of wound healing. BIOMECHANICS AND MODELING IN MECHANOBIOLOGY, 18(5), 1297-1309. doi:10.1007/s10237-019-01145-1

Holmes, J. W. (2019). Model First and Ask Questions Later: Confessions of a Reformed Experimentalist. JOURNAL OF BIOMECHANICAL ENGINEERING-TRANSACTIONS OF THE ASME, 141(7). doi:10.1115/1.4043432

Cohen, N., Deshpande, V. S., Holmes, J. W., & McMeeking, R. M. (2019). A microscopically motivated model for the remodeling of cardiomyocytes. BIOMECHANICS AND MODELING IN MECHANOBIOLOGY, 18(4), 1233-1245. doi:10.1007/s10237-019-01141-5

Rikard, S. M., Athey, T. L., Nelson, A. R., Christiansen, S. L. M., Lee, J. -J., Holmes, J. W., . . . Saucerman, J. J. (2019). Multiscale Coupling of an Agent-Based Model of Tissue Fibrosis and a Logic-Based Model of Intracellular Signaling. FRONTIERS IN PHYSIOLOGY, 10. doi:10.3389/fphys.2019.01481

Kim, A. S., Witzenburg, C. M., Conaway, M., Vergales, J. E., Holmes, J. W., L'Ecuyer, T. J., & Dean, P. N. (2019). Trajectory of right ventricular indices is an early predictor of outcomes in hypoplastic left heart syndrome. CONGENITAL HEART DISEASE, 14(6), 1185-1192. doi:10.1111/chd.12834

Witzenburg, C. M., & Holmes, J. W. (2019). The Impact of Hemodynamic Reflex Compensation Following Myocardial Infarction on Subsequent Ventricular Remodeling. JOURNAL OF BIOMECHANICAL ENGINEERING-TRANSACTIONS OF THE ASME, 141(9). doi:10.1115/1.4043867

Salimova, E., Nowak, K. J., Estrada, A. C., Furtado, M. B., McNamara, E., Quang, N., . . . Rosenthal, N. A. (2019). Variable outcomes of human heart attack recapitulated in genetically diverse mice. NPJ REGENERATIVE MEDICINE, 4. doi:10.1038/s41536-019-0067-6

French, B. A., & Holmes, J. W. (2019). Implications of scar structure and mechanics for post-infarction cardiac repair and regeneration. EXPERIMENTAL CELL RESEARCH, 376(1), 98-103. doi:10.1016/j.yexcr.2019.01.001

Richardson, W. J., Kegerreis, B., Thomopoulos, S., & Holmes, J. W. (2018). Potential strain-dependent mechanisms defining matrix alignment in healing tendons. BIOMECHANICS AND MODELING IN MECHANOBIOLOGY, 17(6), 1569-1580. doi:10.1007/s10237-018-1044-5

Witzenburg, C. M., & Holmes, J. W. (2018). Predicting the Time Course of Ventricular Dilation and Thickening Using a Rapid Compartmental Model. JOURNAL OF CARDIOVASCULAR TRANSLATIONAL RESEARCH, 11(2), 109-122. doi:10.1007/s12265-018-9793-1

Lindsey, M. L., Bolli, R., Canty, J. M. J., Du, X. -J., Frangogiannis, N. G., Frantz, S., . . . Heusch, G. (2018). Guidelines for experimental models of myocardial ischemia and infarction. AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY, 314(4), H812-H838. doi:10.1152/ajpheart.00335.2017

Chen, K., Hu, X., Blemker, S. S., & Holmes, J. W. (2018). Multiscale computational model of Achilles tendon wound healing: Untangling the effects of repair and loading. PLOS COMPUTATIONAL BIOLOGY, 14(12). doi:10.1371/journal.pcbi.1006652

Caggiano, L. R., Lee, J. -J., & Holmes, J. W. (2018). Surgical reinforcement alters collagen alignment and turnover in healing myocardial infarcts. AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY, 315(4), H1041-H1050. doi:10.1152/ajpheart.00088.2018

Holmes, J. W., & Lumens, J. (2018). Clinical Applications of Patient-Specific Models: The Case for a Simple Approach. JOURNAL OF CARDIOVASCULAR TRANSLATIONAL RESEARCH, 11(2), 71-79. doi:10.1007/s12265-018-9787-z

Chen, K., Vigliotti, A., Bacca, M., McMeeking, R. M., Deshpande, V. S., & Holmes, J. W. (2018). Role of boundary conditions in determining cell alignment in response to stretch. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 115(5), 986-991. doi:10.1073/pnas.1715059115

Witzenburg, C. M., & Holmes, J. W. (2017). A Comparison of Phenomenologic Growth Laws for Myocardial Hypertrophy. JOURNAL OF ELASTICITY, 129(1-2), 257-281. doi:10.1007/s10659-017-9631-8

Auger, D. A., Bilchick, K. C., Gonzalez, J. A., Cui, S. X., Holmes, J. W., Kramer, C. M., . . . Epstein, F. H. (2017). Imaging Left-Ventricular Mechanical Activation in Heart Failure Patients Using Cine DENSE MRI: Validation and Implications for Cardiac Resynchronization Therapy. JOURNAL OF MAGNETIC RESONANCE IMAGING, 46(3), 887-896. doi:10.1002/jmri.25613

Phung, T. -K. N., Moyer, C. B., Norton, P. T., Ferguson, J. D., & Holmes, J. W. (2017). Effect of ablation pattern on mechanical function in the atrium. PACE-PACING AND CLINICAL ELECTROPHYSIOLOGY, 40(6), 648-654. doi:10.1111/pace.13086

Zeigler, A. C., Richardson, W. J., Holmes, J. W., & Saucerman, J. J. (2016). A computational model of cardiac fibroblast signaling predicts context-dependent drivers of myofibroblast differentiation. JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY, 94, 72-81. doi:10.1016/j.yjmcc.2016.03.008

Richardson, W. J., & Holmes, J. W. (2016). Emergence of Collagen Orientation Heterogeneity in Healing Infarcts and an Agent-Based Model. BIOPHYSICAL JOURNAL, 110(10), 2266-2277. doi:10.1016/j.bpj.2016.04.014

Spinale, F. G., Frangogiannis, N. G., Hinz, B., Holmes, J. W., Kassiri, Z., & Lindsey, M. L. (2016). Crossing Into the Next Frontier of Cardiac Extracellular Matrix Research. CIRCULATION RESEARCH, 119(10), 1040-1045. doi:10.1161/CIRCRESAHA.116.309916

Holmes, J. W., & Wagenseil, J. E. (2016). Special Issue: Spotlight on the Future of Cardiovascular Engineering: Frontiers and Challenges in Cardiovascular Biomechanics. JOURNAL OF BIOMECHANICAL ENGINEERING-TRANSACTIONS OF THE ASME, 138(11). doi:10.1115/1.4034873

Zeigler, A. C., Richardson, W. J., Holmes, J. W., & Saucerman, J. J. (2016). Computational modeling of cardiac fibroblasts and fibrosis. JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY, 93, 73-83. doi:10.1016/j.yjmcc.2015.11.020

Clarke, S. A., Richardson, W. J., & Holmes, J. W. (2016). Modifying the mechanics of healing infarcts: Is better the enemy of good?. JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY, 93, 115-124. doi:10.1016/j.yjmcc.2015.11.028

Holmes, J. W., Laksman, Z., & Gepstein, L. (2016). Making better scar: Emerging approaches for modifying mechanical and electrical properties following infarction and ablation. PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, 120(1-3), 134-148. doi:10.1016/j.pbiomolbio.2015.11.002

Richardson, W. J., & Holmes, J. W. (2015). Why Is Infarct Expansion Such an Elusive Therapeutic Target?. JOURNAL OF CARDIOVASCULAR TRANSLATIONAL RESEARCH, 8(7), 421-430. doi:10.1007/s12265-015-9652-2

Richardson, W. J., Clarke, S. A., Quinn, T. A., & Holmes, J. W. (2015). Physiological Implications of Myocardial Scar Structure. COMPREHENSIVE PHYSIOLOGY, 5(4), 1877-1909. doi:10.1002/cphy.c140067

Clarke, S. A., Goodman, N. C., Ailawadi, G., & Holmes, J. W. (2015). Effect of Scar Compaction on the Therapeutic Efficacy of Anisotropic Reinforcement Following Myocardial Infarction in the Dog. JOURNAL OF CARDIOVASCULAR TRANSLATIONAL RESEARCH, 8(6), 353-361. doi:10.1007/s12265-015-9637-1

Moyer, C. B., Norton, P. T., Ferguson, J. D., & Holmes, J. W. (2015). Changes in Global and Regional Mechanics Due to Atrial Fibrillation: Insights from a Coupled Finite-Element and Circulation Model. ANNALS OF BIOMEDICAL ENGINEERING, 43(7), 1600-1613. doi:10.1007/s10439-015-1256-0

Lin, D., French, B. A., Xu, Y., Hossack, J. A., & Holmes, J. W. (2015). AN ULTRASOUND-DRIVEN KINEMATIC MODEL FOR DEFORMATION OF THE INFARCTED MOUSE LEFT VENTRICLE INCORPORATING A NEAR-INCOMPRESSIBILITY CONSTRAINT. ULTRASOUND IN MEDICINE AND BIOLOGY, 41(2), 532-541. doi:10.1016/j.ultrasmedbio.2014.09.002

Parker, K. M., Clark, A. P., Goodman, N. C., Glover, D. K., & Holmes, J. W. (2015). Comparison of Quantitative Wall-Motion Analysis and Strain for Detection of Coronary Stenosis with Three-Dimensional Dobutamine Stress Echocardiography. ECHOCARDIOGRAPHY-A JOURNAL OF CARDIOVASCULAR ULTRASOUND AND ALLIED TECHNIQUES, 32(2), 349-360. doi:10.1111/echo.12636

Bilchick, K. C., Kuruvilla, S., Hamirani, Y. S., Ramachandran, R., Clarke, S. A., Parker, K. M., . . . Epstein, F. H. (2014). Impact of Mechanical Activation, Scar, and Electrical Timing on Cardiac Resynchronization Therapy Response and Clinical Outcomes. JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY, 63(16), 1657-1666. doi:10.1016/j.jacc.2014.02.533

Parker, K. M., Bunting, E., Malhotra, R., Clarke, S. A., Mason, P., Darby, A. E., . . . Bilchick, K. C. (2014). Postprocedure Mapping of Cardiac Resynchronization Lead Position Using Standard Fluoroscopy Systems: Implications for the Nonresponder with Scar. PACE-PACING AND CLINICAL ELECTROPHYSIOLOGY, 37(6), 757-767. doi:10.1111/pace.12344

Rouillard, A. D., & Holmes, J. W. (2014). Mechanical Boundary Conditions Bias Fibroblast Invasion in a Collagen-Fibrin Wound Model. BIOPHYSICAL JOURNAL, 106(4), 932-943. doi:10.1016/j.bpj.2013.12.002

Haggart, C. R., Ames, E. G., Lee, J. K., & Holmes, J. W. (2014). Effects of stretch and shortening on gene expression in intact myocardium. PHYSIOLOGICAL GENOMICS, 46(2), 57-65. doi:10.1152/physiolgenomics.00103.2013

Rouillard, A. D., & Holmes, J. W. (2014). Coupled agent-based and finite-element models for predicting scar structure following myocardial infarction. PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, 115(2-3), 235-243. doi:10.1016/j.pbiomolbio.2014.06.010

Kenwood, B. M., Weaver, J. L., Bajwa, A., Poon, I. K., Byrne, F. L., Murrow, B. A., . . . Hoehn, K. L. (2014). Identification of a novel mitochondria! uncoupler that does not depolarize the plasma membrane. MOLECULAR METABOLISM, 3(2), 114-123. doi:10.1016/j.molmet.2013.11.005

Moyer, C. B., Helm, P. A., Clarke, C. J., Budge, L. P., Kramer, C. M., Ferguson, J. D., . . . Holmes, J. W. (2013). Wall-Motion Based Analysis of Global and Regional Left Atrial Mechanics. IEEE TRANSACTIONS ON MEDICAL IMAGING, 32(10), 1765-1776. doi:10.1109/TMI.2013.2264062

Ames, E. G., Lawson, M. J., Mackey, A. J., & Holmes, J. W. (2013). Sequencing of mRNA identifies re-expression of fetal splice variants in cardiac hypertrophy. JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY, 62, 99-107. doi:10.1016/j.yjmcc.2013.05.004

Fomovsky, G. M., Rouillard, A. D., & Holmes, J. W. (2012). Regional mechanics determine collagen fiber structure in healing myocardial infarcts. JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY, 52(5), 1083-1090. doi:10.1016/j.yjmcc.2012.02.012

Ateshian, G. A., Morrison, B. I. I. I., Holmes, J. W., & Hung, C. T. (2012). Mechanics of cell growth. MECHANICS RESEARCH COMMUNICATIONS, 42, 118-125. doi:10.1016/j.mechrescom.2012.01.010

Chandran, P. L., Paik, D. C., & Holmes, J. W. (2012). Structural Mechanism for Alteration of Collagen Gel Mechanics by Glutaraldehyde Crosslinking. CONNECTIVE TISSUE RESEARCH, 53(4), 285-297. doi:10.3109/03008207.2011.640760

Holmes, J. W., & Geest, J. P. V. (2012). Cardiovascular solid mechanics grows and remodels. JOURNAL OF BIOMECHANICS, 45(5), 727. doi:10.1016/j.jbiomech.2011.11.011

Rouillard, A. D., & Holmes, J. W. (2012). Mechanical regulation of fibroblast migration and collagen remodelling in healing myocardial infarcts. JOURNAL OF PHYSIOLOGY-LONDON, 590(18), 4585-4602. doi:10.1113/jphysiol.2012.229484

Fomovsky, G. M., Clark, S. A., Parker, K. M., Ailawadi, G., & Holmes, J. W. (2012). Anisotropic Reinforcement of Acute Anteroapical Infarcts Improves Pump Function. CIRCULATION-HEART FAILURE, 5(4), 515-522. doi:10.1161/CIRCHEARTFAILURE.111.965731

Sharafi, B., Ames, E. G., Holmes, J. W., & Blemker, S. S. (2011). Strains at the myotendinous junction predicted by a micromechanical model. JOURNAL OF BIOMECHANICS, 44(16), 2795-2801. doi:10.1016/j.jbiomech.2011.08.025

Fomovsky, G. M., Macadangdang, J. R., Ailawadi, G., & Holmes, J. W. (2011). Model-Based Design of Mechanical Therapies for Myocardial Infarction. JOURNAL OF CARDIOVASCULAR TRANSLATIONAL RESEARCH, 4(1), 82-91. doi:10.1007/s12265-010-9241-3

Herz, S. L., Hasegawa, T., Makaryus, A. N., Parker, K. M., Homma, S., Wang, J., & Holmes, J. W. (2010). Quantitative Three-Dimensional Wall Motion Analysis Predicts Ischemic Region Size and Location. ANNALS OF BIOMEDICAL ENGINEERING, 38(4), 1367-1376. doi:10.1007/s10439-009-9880-1